Biogenic reefs are of ecological importance due to the high levels of biodiversity they support and the valuable ecosystem services they provide. These reefs have limited distributions, are vulnerable to anthropogenic damage and their natural recovery has been estimated to be very slow. This project therefore aimed to develop restoration techniques that accelerate the natural recovery of biogenic reefs created by Serpula vermicularis (L.) (Polychaeta: Serpulidae), Limaria hians (G.) (Mollusca: Limacea) and Modiolus modiolus (L.) (Mollusca: Bivalvia) all three of which are of conservation importance in the North-East Atlantic. This aim was achieved through trials of novel restoration techniques to assess their potential for future larger scale restoration attempts. The addition of hard substrate proved a reliable restoration technique for all three of the study species. In particular, substrates providing structural complexity supported the highest abundance of recruits. Other restoration techniques, including stock enhancement and substrate stabilisation were found to be less effective. The timing for the deployment for these substrates was also shown to effect the abundance of S. vermicularis recruits, with materials deployed in July having 61 % more colonists than materials deployed in November. The location of deployed substrates within the Loch Creran, Scotland were also shown to create differences in S. vermicularis recruitment, with sites away from existing reefs having 72 % more recruits than sites within existing reef areas. Differences in the effectiveness of restoration treatments between sites was also observed for M. modiolus, with Loch Creran and Scapa Flow sites having on average 1.15 and 1.03 juveniles per restoration unit respectively, compared to 70 juveniles per unit at the site north of Lleyn Peninsula, Wales. The project also highlights taxonomic problems with the identification of juvenile M. modiolus, before providing a robust method validated using DNA barcoding techniques to differentiation M. modiolus from other juvenile bivalves. Whilst the project suggests that the successful restoration of these three biogenic reef-forming species is achievable, it also highlights that the first step in any restoration project must be the removal of pressures on that habitat. The substantial decline in the L. hians reef off Port Appin, Scotland from 40.5 hectares in 2006 to just 2.73 hectares in 2015 shows that without this first step any attempted restoration project would not succeed.

The aim of this study is to assess the biodiversity of the reef cryptofauna (with a focus on the decapods, Crustacea) on dead coral microhabitats, and to begin to understand the processes underpinning their community structure in the Chagos Archipelago. The majority of reef biodiversity is comprised of the cryptofauna, defined as small, often cryptic, mainly invertebrates, which inhabit the reef structure. Despite this the cryptofauna are severely understudied relative to the fish and coral faunal components. An estimated 168,000 species of reef invertebrates have been described on coral reefs, and approximately 20% of reef invertebrates are crustaceans, making them one of the most speciose taxa on coral reefs. The Chagos Archipelago represents one of the most resilient reefs globally, partly because of its remote location, away from the majority of human pressures. Consequently, it serves as an unaffected reference site for biodiversity and ecosystem function studies. The decapod species richness estimate for Chagos (at least 217 species) exceeds that of any other location globally. A high proportion (32%) were observed to be rare species (singletons), this may be an artefact of incomplete sampling, however if this observation represents true rarity it would suggest this component of biodiversity could be more vulnerable to biodiversity loss than previously thought. Furthermore, any biodiversity loss could also have implications for ecosystem function if rare species contribute disproportionately more to vulnerable ecosystem processes than dominant species. Data presented on determining the most accurate species delimitation method for estimating decapod species richness utilising DNA barcoding. Performance of species delimitation methods was taxon-specific within the decapods, and delimitation of singletons was challenging for all methods. However, the Poisson tree processes (PTP) approach was generally the most accurate at delimiting decapod putative species. Whilst assessing decapod diversity a high prevalence of obligate coral-dwellers on dead coral microhabitats were discovered. Obligate coral-dwellers are almost universally found on live coral, inferring they have a strong reliance on live coral for food, habitat and/or recruitment. The prevalence of obligate coral-dwellers on dead coral suggests that these decapods are not simply persisting on coral hosts that have died but may be explicitly recruiting to or moving to dead coral hosts at certain stages in their life cycle. Finally, the processes influencing community assembly and maintenance of a family of decapods, the Palaemonidae, on dead coral colonies was investigated. There was spatial hierarchy in trait and phylogenetic diversity, with environmental filtering acting only at the local level (within atolls and between coral colonies). Whilst phylogenetic signal at the metacommunity level (the archipelago) was inconclusive, trait convergence and lability of trait evolution were key processes determining species distribution at the local level. This thesis represents the first biodiversity estimation of the cryptofauna in Chagos on any microhabitat and subsequently provides a baseline against which to compare this component of biodiversity in other areas experiencing higher levels of anthropogenic stressors, at least in the Indian Ocean. I also produce a rare empirical evaluation of species delimitation methods, which will provide guidance for future decapod molecular studies. The prevalence of obligate coral-dwellers on dead corals demonstrates the complexity of these organisms' habitat associations and highlights the need for further investigation to establish their vulnerability to habitat degradation on coral reefs. Furthermore the identification of some of the deterministic processes driving community structure of the Palaemonidae contributes to understanding of ecosystem function.

Tidal mixing fronts establish during the summer months over shelf-seas, and separate tidally-mixed from stratified water masses. They play an important part in shelf-sea bio-physical processes, including volume transport and facilitation of primary productivity. Frontal hydrodynamics provide the physical necessities for prey aggregations to develop, holding the potential for biodiversity hotspots. However, there is limited knowledge on long-term variability of tidal mixing fronts and its effect on associated ecosystems, due to a lack of adequate datasets. Such information would greatly benefit spatial conservation efforts and improve our understanding of ecosystem dynamics on the continental shelf. Satellite-derived frontal maps and extensive biological datasets (from 1990-2010) are employed here to investigate spatio-temporal variability of tidal mixing fronts and their significance for shelf-sea biology from zooplankton tomegavertebrates in the Celtic Sea. In addition, this study assesses the suitability and limitations of satellite-derived frontal metrics for quantitative analyses and employs innovative technology (submarine gliders) to fill data gaps in species-environment interactions. This research provides guidance on the use of frontal metrics in quantitative analysis, such as the need to account for data variability over the years and the careful consideration of the employed frontal metric. This thesis furthermore, represents the first description of long-term temporal variability of tidal mixing fronts on the European shelf and highlights a potential sensitivity to climate change due to positive correlations with rising temperatures. Consequences could include extension of the frontal season and intensification of the frontal density gradient with knock-on effects on associated biota. The density gradient of tidal mixing fronts was shown to act as a direct distribution boundary for plankton between different shelf-sea domains. Climate-change-driven shifts in the seasonality of these fronts may have a direct impact on dispersal of passive floating organisms, habitat connectivity and adult populations of species with planktonic larvae, including commercially important fish and the benthos. Apart from a barrier function, fronts were also found to be important foraging areas for specialist megavertebrates, which were strongly associated with persistent frontal areas, whereas generalist feeders were not. Tidal mixing fronts represent suitable conservation areas for sensitive species in shelf-seas. The underlying mechanisms leading to bio-aggregations at these sites require more research. High-resolution data, simultaneously collected across multiple trophic levels can be obtained by autonomous robotic fleets in the near future.

Although our knowledge on the vast deep-sea biome has increased in recent decades, we still have a poor understanding of the processes regulating deep-sea diversity and assemblage composition, as well as their underlying natural variability in space and time. In the face of unprecedented anthropogenic impact on this environment, addressing this knowledge gap remains of paramount importance. In this thesis I focus on the effect of mesoscale (10s of kilometres) spatial heterogeneity, in the form of abyssal hills and surrounding abyssal plains, on benthic communities and specifically on foraminiferal faunas living at abyssal depths in the northeast Atlantic. ‘Live’ (Rose-Bengal-stained) and dead benthic foraminiferal assemblages, including rarely-studied soft-walled monothalamous species, were analysed based on a total of 16 Megacorer samples (0.25 cm2 surface area, 0-1 sediment horizon, >150 ?m sieve fraction) from five sites within the area of the Porcupine Abyssal Plain Sustained Observatory (PAP-SO, NE Atlantic, ~4850 m water depth). Three sites were located on the tops of small abyssal hills (~200-500 m elevation) and two on the adjacent abyssal plain. The main results of this analysis include the following. (1) Description of new morphotypes of poorly known primitive benthic foraminifera associated with (i.e. sessile on) planktonic foraminiferal shells and mineral grains. Some of these forms were more common on the hills, while others were more common on the plain. (2) Agglutinated foraminifera selected particles of different sizes on the hills compared to the plain, which affected their test morphometry and visual appearance. Distinct hydrodynamic conditions, and consequently distinct sediment granulometric characteristics between the two settings (hills, plain) resulted in foraminifera on the hills having more coarsely agglutinating tests. This information could be useful in palaeoecological interpretations of the fossil record. (3) Live benthic foraminiferal assemblages were significantly influenced by seafloor topography. Abyssal hills had a higher species density compared to the plain, supported a distinct fauna, and therefore tended to increase regional diversity. Enhanced bottom-water flow on hills, which affects organic matter supply and local sedimentology, were proposed to be responsible for these differences. (4) During the transition from live to dead benthic foraminiferal faunas there was a significant loss of delicate agglutinated and organic-walled forms. Unlike ‘live’ assemblages, the composition of the dead assemblages was very similar in hill and plain settings, suggesting that it would not be possible for paleoceanographers to differentiate between fossil foraminiferal faunas originating from these topographically contrasting settings. In conclusion, this study highlighted the significant effect of hills on agglutination patterns, assemblage composition and regional diversity of living benthic foraminifera. Since abyssal hills are one of the most common landforms on Earth, their presence may substantially enhance abyssal biodiversity, with important implications of deep-sea ecosystem functioning.

No description available.

No description available.

Sustaining an environment which conveys a high resilience to reef corals is critical in order to mitigate the immediate threat of climate change to reef ecosystems. The nutrient environment plays a significant role in sustaining the stability of the coral-zooxanthellae symbiosis, making anthropogenic nutrient pollution as well as the climate change driven nutrient impoverishment of oceanic waters pressing threats to coral reef persistence. Yet, many aspects of coral nutrient biology remain poorly understood, impeding science driven management strategies. This thesis aimed to advance our knowledge on how different nutrient environments affect the functioning of the coral-algal symbiosis by teasing apart the interacting effects of two principal nutrient sources (dissolved inorganic nutrient uptake and heterotrophic feeding), as well as of the two essential nutrients, nitrogen and phosphorus, both in dissolved inorganic and particulate organic forms. This was achieved through long-term exposure (up to 1.5 years) of the Euphyllia paradivisa-clade C1 Symbiodinium association to replete (+N+P), limited (-N-P), or imbalanced (+N-P/-N+P) dissolved inorganic nutrient availabilities in combination with targeted host feeding with balanced or nitrogen enriched prey items. Thereby, this work stood apart from past investigations by yielding definitive phenotypes representative of different nutrient availabilities. Moreover, the importance of food quality when considering the benefit of heterotrophy to reef corals had previously been overlooked. Findings suggest that heterotrophy provides a greater benefit to the coral host than to the symbiont and is unable to compensate for diminished dissolved inorganic nutrient availability, demonstrating a significantly greater dependence of the symbiosis to the latter nutrient source. A balanced N/P ratio, both in dissolved inorganic and particulate organic form, was shown to be essential for the stability of the symbiosis and for the nutritional benefit provided by heterotrophy. Particularly nitrogen enrichment resulted in severe nutrient stress and compromised thermal stress resilience, implying a vital reliance on a continued supply of phosphorus and emphasising the necessity of managing nitrogen pollution and monitoring N/P ratios. Zooxanthellae ultrastructural biomarkers established in this thesis (cell size, lipid body, starch granule and uric acid crystal accumulation, accumulation body fragmentation) hold potential for the aid in the identification of, and discrimination between different forms of nutrient stress in reef corals. Yet, ultimately corals need to adapt to warmer oceans. Diverse Symbiodinium genotypes convey varied thermal tolerance to their coral host. Yet, the mechanisms underpinning their thermal sensitivity remain largely elusive. The second aim of this thesis was to examine the role played by the algal membrane composition. The intact polar lipid biochemistry of a thermally-sensitive (clade C) and -tolerant (clade D) type were characterised by HPLC-ESI tandem mass spectrometry. Distinctions in chloroplast membrane composition could be related to differential inherent thermal tolerance. Moreover, vast differences in the lipid biochemistry of extraplastidic membranes were identified, exemplifying unprecedented metabolic differences among Symbiodinium clades. Biochemical markers of a thermally tolerant phenotype (MGDG/DGDG ratio, glycolipid saturation) could advance our understanding and projections of the potential of reef corals to acclimate and adapt to future climate change scenarios.

The Earth's climate is changing at a pace that was never observed before, and this may result in species migration to new habitats or, more drastically, to extinction. Nevertheless, certain species which have a fast turnover might evolve and become resilient to the effects of a rapidly changing environment. This resiliency-scenario better applies to species with large population size and rapid generation times, such as the coccolithophore Emiliania huxleyi, which plays a fundamental role in the marine ecosystem since it produces calcium carbonate coccoliths and it is responsible of circa 80% of carbonate precipitation in seawater. E. huxleyi shows both morphological and genetic intraspecific variability, with A and B being its two main coccolith morphological types, corresponding to its two main genotypes characterised by coccolith morphology motif (CMM) I & II respectively. Here I present the results of a temporal and geographical study, aimed to investigate the extant diversity of E. huxleyi in both the Northern and Southern hemispheres and its genetic standing stock over a 6-year time period. I found that only genotypes CMM I & CMM IV persist and dominate throughout the years, and they are both representative of E. huxleyi A morphotype, which dominates North-eastern Atlantic, Western English Channel (WEC) and North Sea E. huxleyi bloom events. Additionally, my study confirms the genetic variability in the global E. huxleyi community and reveals that the intraspecific variability is defined by geophysical features, with E. huxleyi morphotype A being dominant in temperate regions (10-18 °C), while morphotypes B & B/C as defined by CMM II & IIb, respectively, being dominant in polar regions (< 10 °C). Finally my results show that cultures maintained in laboratory collections might not be representative of real extant stocks, and therefore may not necessarily describe the genetic composition of wild biogeographic populations.

Current trends indicate that key events in the life cycle of marine organisms (e.g. spawning, reproduction, larval release) are taking place earlier in the season in response to global warming associated with climate change. Specific changes in the phenology (i.e. the timing of these life cycle events) of planktonic organisms suggest that responses to climate change are not consistent for all functional groups in the pelagic community. As a result, the tight synchrony that exists between pulses of production of larvae and their food sources could be disrupted; this may cause a decline in survival and affect recruitment levels into a population. Marine invertebrates with complex life cycles from temperate‐cold regions may be particularly sensitive to changes in food availability and temperature as, during the larval phase, many of these species are strongly dependent on seasonal peaks of pelagic food sources. The degree to which mismatches between the timing of larval development and seasonal peaks of planktonic production may influence recruitment success of a species is unknown, and may vary depending on species life‐history. Intertidal barnacles are widely distributed and ecologically important species which serve as a good model species to investigate the impact of potential shifts in food and temperature associated with climate change. Semibalanus balanoides is boreal species which synchronously releases its larvae once a year to coincide with the spring phytoplankton bloom. In contrast, Austrominius modestus is a lusitanean species which releases multiple broods over a much longer period of time, with larval production at its peak during the summer months when food supply is lower. These two contrasting species are ideal models to use in a comparative study aimed at understanding the effects of food limitation and temperature on the recruitment success of marine invertebrates. In this study, I focused on the combined effects of food limitation and temperature on larval performance of S. balanoides and A. modestus. Firstly, I examined whether a reduction in available food at different temperature conditions would have an impact on the recruitment success of either species. This approach was to assess if there were any differences between species responses to potential low food environments and also explored whether changes in temperature could exacerbate any larval responses to low food. I also evaluated the responses of both species to temporal mismatches, simulating food availability as consequence of larval release occurring before or after peaks in food abundance, to identify whether the timing of food availability during larval development was important for recruitment success. Following this, I concentrated on identifying the mechanisms by which these two species may differ in their responses to food limitation and temperature. Here, the tolerance of both species to starvation at different temperatures was examined and the elemental composition of the energy reserves they have upon hatching was assessed to identify any differences that may exist between the species. Finally, I focused on the ingestion rates of both species to see whether they exhibit any differences in their feeding rates in response to a range of food concentrations at different temperatures. A partial energy budget for larvae was also estimated to evaluate if species differed in their capabilities to use food for growth, development and maintenance in different food/temperature environments. Results showed that the timing and abundance of food sources were critical for the recruitment success of S. balanoides and less important for A. modestus. A temperature of 15oC was sub‐optimal for S. balanoides and tended to increase the negative effects of food limitation. Both food limitation and temperature had strong effects on naupliar mortality and cyprid settlement success rates for S. balanoides and, thus, were important in determining the supply and quality of settlers to a population. When compared to A. modestus, the poorer performance of S. balanoides could not be explained by differences in initial energy reserves or starvation tolerance immediately after hatching as these were comparable between the two species. Considerable differences were observed in the ingestion rates of both species during the early stages and suggested that differences in mass specific feeding rates may be linked to the better performance of A. modestus in food limited environments. In summary, results suggest that recruitment success of S. balanoides would be particularly vulnerable to mismatches of larval pulses with their food sources, particularly at higher temperatures, due to the strong effects of these factors on larval supply and larval quality. In contrast, even under food limited conditions, moderate increases in temperature should not result in strong negative consequences for A. modestus. Work presented here highlights that species‐specific responses to climate‐driven changes in the environment may profoundly affect the abundance and distribution of marine invertebrate species with complex life cycles, through direct and interactive effects of these changes on larval mortality and settlement success.

Climate change is directly and indirectly impacting biota, A common prediction is that biogeographic ranges will extend poleward, with increases in abundance near the leading edge. Understanding how marine species will respond is hindered by a scarcity of long-term datasets. However, within the British Isles there is a long history of well-documented intertidal research. Historical data are stored in a variety of forms from grey-literature and national databases to published journals. Sabellaria alveolata is a conservationally important biogenic reef-forming species that reaches its northern range limit within the British Isles. The aim of this thesis was to establish if S. alveolata has responded predictably to climate change, and to investigate abiotic and biotic drivers of observed change. Through comparisons with historical and contemporary collated and collected data on different spatial scales, it was clear that S. alveolata has exhibited persistence in distribution, and stability in abundance and morphology on a long term, broad spatial scale with no significant difference in distribution, abundance or reef-forming morphology exhibited from the 1980s to the 2010s (>50 % stability in all paired data; Bush et al., Chapter 2). Within this, S. alveolata populations have demonstrated change on reduced spatial scales, increasing in response to increased temperature near the northern range edge, with some decreases in response to increased wave exposure well within the range (explaining ~ 50 % of the variance in both instances; Bush et al., Chapter 3). Through long-term monitoring studies, this study demonstrated high within-site variability. Additionally evidence was provided that, within Britain, the intertidal ecosystem engineers S. alveolata and Mytilus edulis are alternative stable state communities on pebble shores, with complete change of state from S. alveolata dominated to M. edulis dominated reef in 1 year (Bush & Davies, Chapter 4). State is partially maintained by settlement success in both instances (R2 ≥ 0.55). Finally, through a combination of traditional monitoring and laboratory techniques with state of the art modelling approaches, this study provided insights into reproductive strategy, larval dispersal and population connectivity patterns of S. alveolata and provided evidence of subpopulations of reef-forming species on British coastlines (e.g. Scotland to North Wales, Mid Wales, and South Wales to Southwest England; Bush et al., Chapter 5).